👀 Summary

The idea

TOFF will automatically give you the topology for your small molecule that you need for Molecular Dynamic Simulation. Usually this task involves a lot of efforts making the QM calculations: get charges, fit dihedral potential, see contribution of the hydration shell and more and more aspects. Open Force Field is a very active initiative and a perfect tool to get rid of these problems. Their force fields are constantly under update. These force fields use the SMIRKS Native Open Force Field (SMIRNOFF) format, which helps to reach a wide number of chemical structures.

Since version 0.1.0, it is also possible to get GAFF and Espaloma force field parameters.

TOFF is python module but also have a friendly command line interface. The main class to work with is toff.utils.Parameterize(). Examples on how to use both interface: as a module and as a command line are found in the Tutorials section.

Input data

The only input needed is the definition of the molecule to parameterize. The molecule could be a valid RDKit molecule (rdkit.Chem.rdchem.Mol()) or any other extension accepted by the function toff.utils.get_rdkit_mol(). In case the command line is used, the inputs are specified through a configuration yaml file (see this YouTube video to get use to yaml file anatomy).